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#
# The Python Imaging Library.
# $Id$
#
# the Image class wrapper
#
# partial release history:
# 1995-09-09 fl Created
# 1996-03-11 fl PIL release 0.0 (proof of concept)
# 1996-04-30 fl PIL release 0.1b1
# 1999-07-28 fl PIL release 1.0 final
# 2000-06-07 fl PIL release 1.1
# 2000-10-20 fl PIL release 1.1.1... | samabhi/pstHealth | venv/lib/python2.7/site-packages/PIL/Image.py | Python | mit | 81,497 | [
"Gaussian"
] | 6a5c262697557ab5198d6180db6d57f1d8973bc1bcfdef24cba1463f9caf6d0e |
from ase import Atom, Atoms
m = Atoms('H2')
a = m[0]
b = Atom('H')
for c in [a, b]:
assert c.x == 0
c.z = 24.0
assert c.position[2] == 24.0
assert c.symbol == 'H'
c.number = 92
assert c.symbol == 'U'
c.symbol = 'Fe'
assert c.number == 26
c.tag = 42
assert c.tag == 42
c.momen... | suttond/MODOI | ase/test/atom.py | Python | lgpl-3.0 | 562 | [
"ASE"
] | fdeae28958255c9674329ad42b0aa1f8a388c475760bcfbe37f84a0349a8b235 |
"""
@name: Modules/Computer/Pi/_test/test_pi_gpio.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2017-2020 by D. Brian Kimmel
@note: Created on Feb 8, 2018
@license: MIT License
@summary:
"""
__updated__ = '2019-12-30'
# ## END DBK
| DBrianKimmel/PyHouse | Project/src/Modules/Computer/Pi/_test/test_pi_gpio.py | Python | mit | 284 | [
"Brian"
] | 739c793b29d0639fc1766dc29888285e0851415f785c2f8c58fc2d79ef142ba5 |
"""
Tests for molecule utilities.
"""
import VMD
from Molecule import Molecule as _Molecule
from pyvmd.molecules import FORMAT_PDB, Molecule, MoleculeManager
from pyvmd.representations import Representation
from .utils import data, PyvmdTestCase
class TestMolecule(PyvmdTestCase):
"""
Test `Molecule` class.
... | ziima/pyvmd | pyvmd/tests/test_molecules.py | Python | gpl-3.0 | 12,476 | [
"VMD"
] | ac5e7c7914df37e899e6d9b6cfacb4be049169715f87d766a1dc0d642c03429e |
"""
Module for rendering Voronoi cells
"""
from __future__ import absolute_import
from __future__ import unicode_literals
import logging
import vtk
import numpy as np
from . import baseRenderer
from . import povrayWriters
from .. import utils
from ...algebra import vectors
class VoronoiRenderer(baseRenderer.BaseR... | chrisdjscott/Atoman | atoman/rendering/renderers/voronoiRenderer.py | Python | mit | 4,312 | [
"VTK"
] | ba746bdd89f4b7352efbcf331dc5b7ab37c571b984d5eef109b69384fe6dc62d |
__author__ = 'squiresrb'
def parse_blast_result(blast_file_path):
from Bio.Blast import NCBIXML
output_file = "%s.alignments.txt" % blast_file_path
output_handle = open(output_file, 'w')
result_handle = open(blast_file_path)
blast_records = NCBIXML.parse(result_handle)
#E_VALUE_THRESH = 0.04
... | parasite-genomics/Pipelines | blast_xml_to_text.py | Python | apache-2.0 | 2,170 | [
"BLAST"
] | d575023d08caa226856636ac2a75f38676217c0b71dd110f9e4533ccd232aa86 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Classes for reading/manipulating/writing exciting input files.
"""
import xml.etree.cElementTree as ET
import numpy as np
import scipy.constants as const
from monty.io import zopen
from monty.json import ... | gmatteo/pymatgen | pymatgen/io/exciting/inputs.py | Python | mit | 15,398 | [
"CRYSTAL",
"exciting",
"pymatgen"
] | 6f4ab60e7ab2c005a6f8140c4c1423018dac3d78ed2b35520656c1ce8e82e606 |
""" This script submits a test production
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
# pylint: disable=wrong-import-position, protected-access
import os
import json
from DIRAC.Core.Utilities.DIRACScript import DIRACScript as Script
Script.parseCo... | ic-hep/DIRAC | tests/System/dirac-test-prod-sys.py | Python | gpl-3.0 | 5,283 | [
"DIRAC"
] | f37747755f33349c0b60399047dd90b92e094b69fd02127662fb7bc07293c9e3 |
#!/usr/bin/env python
import functools
import click
def get_mask_data(depth):
import numpy as np
return np.where(depth > 0, 255, 0).astype(np.uint8)
def smooth_image(data, sigma):
from scipy import ndimage
return ndimage.gaussian_filter(data, sigma=sigma)
def save_image(data, path):
import... | dionhaefner/veros | veros/cli/veros_create_mask.py | Python | mit | 1,384 | [
"Gaussian",
"NetCDF"
] | 7aef41ad85774e3c5b0470aedeaa48add13aadb4df164f38db1ff893c000b715 |
# Copyright (C) 2015 Hydriz Scholz
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in ... | Hydriz/DBReports | reports/inactiveusers.py | Python | gpl-3.0 | 2,500 | [
"VisIt"
] | 330ed461080d97e2b526a3daac5784e33895828993be87c2657d3bc337ff5f2c |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/fci/test/test_spin_op.py | Python | apache-2.0 | 6,460 | [
"PySCF"
] | 4574ec263e35338ee2017ee03ac18008b585388b347663e3e6977ffcc35988ed |
#!/usr/bin/env python
# Copyright 2017 Calico LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or ... | calico/basenji | bin/basenji_motifs_inject.py | Python | apache-2.0 | 8,540 | [
"pysam"
] | b1bec4ac244465e81e72c065ddab209884430f75cc3d555e7cbc92e02fc7c02f |
import autograd.numpy as np
from rdkit import Chem
from util import one_of_k_encoding, one_of_k_encoding_unk
def atom_features(atom):
return np.array(one_of_k_encoding_unk(atom.GetSymbol(),
['C', 'N', 'O', 'S', 'F', 'Si', 'P', 'Cl', 'Br', 'Mg', 'Na',
... | HIPS/neural-fingerprint | neuralfingerprint/features.py | Python | mit | 1,747 | [
"RDKit"
] | d924de328de6d3417c37d22a9c2fb45d23e1e9fbea7da96e10fc8b95923edf62 |
#
# Copyright (C) 2013,2014,2015,2016 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option)... | Marcello-Sega/espresso | src/python/espressomd/highlander.py | Python | gpl-3.0 | 2,374 | [
"ESPResSo"
] | ea8e4715c0f748300e4c0b97ac582ef36e8996a4154d9db3e34886692eef22bd |
#Script to calculate the free energy change
# upon removing a set of host-guest distance
# restraints and applying standard state conditions
# @authors: Stefano Bosisio and Julien Michel
import os,sys, random
import math
from math import pi, cos, sin
from Sire.Tools.OpenMMMD import *
from Sire.Tools import Parameter, ... | chryswoods/Sire | wrapper/Tools/StandardState.py | Python | gpl-2.0 | 17,579 | [
"MDTraj"
] | e03eb7212e4eca77240bfb6ac553fc3d854226f08a15cf3bee30c3605c6a1318 |
## Copyright 2017 Knossos authors, see NOTICE file
##
## Licensed under the Apache License, Version 2.0 (the "License");
## you may not use this file except in compliance with the License.
## You may obtain a copy of the License at
##
## http://www.apache.org/licenses/LICENSE-2.0
##
## Unless required by applicable... | MjnMixael/knossos | knossos/web.py | Python | apache-2.0 | 71,091 | [
"Galaxy"
] | 48dd13f188cb665329911e8ac7322329f2c6ba8aa09b9378e8d7f5b805c4bfd4 |
# -*- coding: utf-8 -*-
"""
Control flow for the AST backend.
Adapted from Cython/Compiler/FlowControl.py
"""
from __future__ import print_function, division, absolute_import
import re
import ast
import copy
from functools import reduce
from numba import error, visitors, symtab, nodes, reporting
from numba import ... | shiquanwang/numba | numba/control_flow/control_flow.py | Python | bsd-2-clause | 40,261 | [
"VisIt"
] | cc8b52178af301c939f7cfca550a2bec93371bba49c9f3cbba13c53683fbb8f0 |
"""MDTraj: A modern, open library for the analysis of molecular dynamics trajectories
MDTraj is a python library that allows users to manipulate molecular dynamics
(MD) trajectories and perform a variety of analyses, including fast RMSD,
solvent accessible surface area, hydrogen bonding, etc. A highlight of MDTraj
is ... | hainm/mdtraj | setup.py | Python | lgpl-2.1 | 10,333 | [
"Amber",
"CHARMM",
"Gromacs",
"MDTraj",
"NAMD",
"NetCDF",
"TINKER"
] | d5d618f34e48cd3ae2da47029043714297a9639ec0925f25920f822092fa2bf0 |
"""
(This script is independent from lfc_dfc_copy)
This script is used to migrate the content of the LFC DB to the DFC DB when used with Stored procedure and Foreign keys.
It won't work with the other schema. It is the central component of the migration.
* Please read the doc of each method in this script, there are... | andresailer/DIRAC | DataManagementSystem/Utilities/lfc_dfc_db_copy.py | Python | gpl-3.0 | 40,839 | [
"DIRAC"
] | 91be4d6b446cb6245e3c900f702d7356cad1188d35ce018eb89ee68fdb5307db |
#
# Copyright 2018 Analytics Zoo Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... | intel-analytics/analytics-zoo | pyzoo/test/zoo/orca/data/test_write_parquet.py | Python | apache-2.0 | 9,137 | [
"ORCA"
] | 28d63b51fc87f9dcc923351fabea9792f675559ba1c6de61abf997afb8b1144f |
# -*- coding: utf-8 -*-
"""
merge.py
RAPIDpy
Created by Tim Whitaker, 2015.
Modified by Alan D Snow, 2015-2016
Copies data from RAPID netCDF output to a CF-compliant netCDF file.
Code originated from Tim Whitaker at University of Texas. The code was
modified by Alan Snow at US Army ERDC.
Remarks:
A ... | erdc-cm/RAPIDpy | RAPIDpy/postprocess/merge.py | Python | bsd-3-clause | 22,399 | [
"NetCDF"
] | 93b94d23c89fb552ae228b869e1fad1cb8cb3255beb71db1074b0de3b63b7326 |
# A list of extensions that different importers support.
from menpo.io.spatial_image import BNTImporter, FIMImporter, ABSImporter
from menpo.io.landmark import (LM3Importer, LANImporter, LM2Importer,
BNDImporter, JSONImporter)
from menpo.io.landmark_mesh import MeshPTSImporter
from menpo.... | karla3jo/menpo-old | menpo/io/extensions.py | Python | bsd-3-clause | 3,843 | [
"ASE"
] | 16511bb9683459e2abb20346f6165b289dcc3605ea6e036d3acebbd710fdc2aa |
# encoding: utf-8
from __future__ import unicode_literals
from nose.tools import assert_equal, assert_less_equal
from . import split_tweet
_TESTS = [
("I'm not sure what to do", 23, ["I'm not sure what to do"]),
("I'm not sure what to do", 22, ["1/2 I'm not sure what", "2/2 to do"]),
("I'm not sure what... | paulfurley/python-tweet-splitter | tweetsplitter/test_split_tweet.py | Python | mit | 1,347 | [
"exciting"
] | 4c91d8a0d910f577149ed36764bb0136b0a6e3926533fa4a2b916a3838e581e9 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2016, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Facilities for moving parsed data to other cheminformatic libraries."""
try:
import openbabel
except ImportError:
... | Schamnad/cclib | src/cclib/bridge/__init__.py | Python | bsd-3-clause | 591 | [
"cclib"
] | ad3b1af8f4aec89499e9d9e96ecdecf849437464bf88f19f19440c9ebfc90c3c |
from __future__ import annotations
import logging
import math
from scitbx.matrix import col, sqr
from dials.algorithms.indexing import DialsIndexError
from dials.array_family import flex
logger = logging.getLogger(__name__)
"""
Class to determine mosaicity and effective domain size for a crystal given a set of inde... | dials/dials | algorithms/indexing/nave_parameters.py | Python | bsd-3-clause | 9,929 | [
"CRYSTAL"
] | e5e912cdfb26ade0ba38c73db91710113b32dd0047d3e9f6a17c2d0deaedcf42 |
# -*- coding: utf-8 -*-
"""
Created on April 11, 2012
@author: Isabel Restrepo
"""
# Computes the gaussian gradients on a boxm_alpha_scene
import os;
import optparse;
import time;
import sys;
import numpy as np
import matplotlib
matplotlib.use("TkAgg")
import matplotlib.pyplot as plt
import glob
#plot k_means runnin... | mirestrepo/voxels-at-lems | jstsp11/plot_running_times.py | Python | bsd-2-clause | 7,956 | [
"Gaussian"
] | f285d5a754c19b9eedfcde8132d6ab14a2551998236d1f7e892967635f3e084d |
# Copyright 2018 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | davidzchen/tensorflow | tensorflow/python/distribute/input_lib.py | Python | apache-2.0 | 78,513 | [
"VisIt"
] | 5d618d569670ab708ff0a416d72846a2fb9c8086937f36edecb3d7553f5e71eb |
""" $lic$
Copyright (C) 2016-2020 by Tsinghua University and The Board of Trustees of
Stanford University
This program is free software: you can redistribute it and/or modify it under
the terms of the Modified BSD-3 License as published by the Open Source
Initiative.
This program is distributed in the hope that it wi... | stanford-mast/nn_dataflow | nn_dataflow/core/layer.py | Python | bsd-3-clause | 12,298 | [
"NEURON"
] | 6ed7087107cfee11850e05adeb0c3ee7872520fd0e62b4f11c85104996e9eaf9 |
#
# Copyright (C) 2020 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later vers... | pkreissl/espresso | testsuite/python/p3m_tuning_exceptions.py | Python | gpl-3.0 | 20,230 | [
"ESPResSo"
] | 81fdbb442b486aa23e32e22b5507c55fbc520ef70479fe4aeb190c8e45d79e35 |
#!/usr/bin/python
#
# Copyright 2015 John Kendrick
#
# This file is part of PDielec
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the MIT License
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied wa... | JohnKendrick/PDielec | PDielec/GulpOutputReader.py | Python | mit | 15,555 | [
"GULP"
] | 0ded6aad67b777993920301d93146cbb5eda7bda63906e0b62abb34c0ea95f13 |
import numpy as np
def expand_region_by(mask, frac):
import scipy.ndimage
N = np.sum(mask)
for sig in range(1, 20):
# convolve mask with a gaussian
mask_out = scipy.ndimage.filters.gaussian_filter(mask.copy().astype(np.float), sig, mode = 'constant')
# progressively truncate u... | andyofmelbourne/crappy-crystals | utils/padding.py | Python | gpl-3.0 | 666 | [
"Gaussian"
] | c1c310ae4766b84510967134ffff9711487e2a6837b2945c89c8620b7d8f250a |
from __future__ import division, print_function
from __future__ import absolute_import
from __future__ import unicode_literals
import pickle as pickle
from sympy.matrices import Matrix
from sympy import sympify
import sys
from .ccobjects import CCBase
from ...utils.misc import extract_model
from ...utils.misc import ... | PySCeS/PyscesToolbox | psctb/analyse/_symca/_symca.py | Python | bsd-3-clause | 15,450 | [
"PySCeS"
] | 4409404a93fe7254f1241fe8588f5a8a756a7a993e1cda9164864b1511df31db |
# This file is part of turbulucid
# (c) 2018 Timofey Mukha
# The code is released under the GNU GPL Version 3 licence.
# See LICENCE.txt and the Legal section in the README for more information
from __future__ import print_function
from __future__ import division
import vtk
from vtk.numpy_interface import dataset_adap... | timofeymukha/turbulucid | tests/core/test_readers.py | Python | gpl-3.0 | 6,753 | [
"VTK"
] | c96bca12cc93b3c3bf6d344394e396d6393599526eb765fee4a27732f17a451d |
#!/usr/bin/env python
import os
import numpy as np
from ..streamlines.track_dataset import RegionCluster, TrackDataset
from .cluster_ui import ClusterEditor, ClusterAdapter
from ..streamlines.track_math import tracks_to_endpoints
from ..database.track_datasource import TrackDataSource
from traitsui.editors.tabular_edit... | mattcieslak/DSI2 | dsi2/aggregation/region_labeled_clusters.py | Python | gpl-3.0 | 28,840 | [
"Mayavi"
] | 44d03d6054dd1bbff34971ab681f2969218eef06bddd1fbfdec4872ac24b16b7 |
#! /usr/bin/env python
# D.J. Bennett
# 29/04/2015
"""
Set dependencies for pG-lt
"""
import sys
import os
import subprocess
import re
import argparse
import pickle
from tabulate import tabulate
from pglt import _RAXML as raxml
from pglt import _MAFFT as mafft
from pglt import _MAFFTQ as mafftq
from pglt import _MAFFTX... | DomBennett/pG-lt | pglt_set_dependencies.py | Python | gpl-2.0 | 5,504 | [
"BLAST"
] | bb2db3256bc0d9e613f3e670e2358bd693df5dc31691b221bfd06213d57bb4db |
#!/usr/bin/env python
# -*- coding: utf8 -*-
import codecs
import os
import pickle
import random
import time
from . import find_git_repos
from . import git_util
def init_ignore(ignore_filename='.git_update_all_ignore'):
ignore_set = {'.cache', '.git', '$RECYCLE.BIN',}
if os.path.exists(ignore_filename):
... | autodrive/utils3 | utils3/git_update_all.py | Python | apache-2.0 | 9,873 | [
"VisIt"
] | 048df5e76a5436c8b2e336bdd922353a13caa0a93729bfc7594e6856518b49be |
import sys, time
sys.path.append("../../")
sys.path.append("../")
import numpy as np
import pylab as p
import scipy.stats.distributions as s
#Display
from tikz_graphs import StateGraphParams, StateGraph
from utils import Utils, PhraseUtils
"""
* Nog uitstaande vir Grid2:
* Make seker Gaussian offset is reg en alle ... | singleswitch/ticker | experiments/simulations/grid_simulation.py | Python | mit | 40,431 | [
"Gaussian"
] | 8a68f758761e87743eae2e55f2b69c1f862f638f6389ae4fbcce7bf66912ed86 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | apache/climate | obs4MIPs/factory/formats.py | Python | apache-2.0 | 18,450 | [
"NetCDF"
] | 607ffdc7cbecd29e0522a389ef359e6ea1f5d817aa87403865c575166efbf16c |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RRhdf5(RPackage):
"""R Interface to HDF5
This package provides an interface betwee... | LLNL/spack | var/spack/repos/builtin/packages/r-rhdf5/package.py | Python | lgpl-2.1 | 1,809 | [
"Bioconductor"
] | d8a92c86fcf3850c232063773df3ca209c34f60abb5a83dcf854db1c7a08d996 |
# from datetime import date, timedelta
#
# from django.test import TestCase, tag
#
# from edc_constants.constants import NEG, POS, UNK, YES, IND, NAIVE, NO, DEFAULTER, ON_ART
#
# from bcpp_subject.old_subject_helper import SubjectHelper, ART_PRESCRIPTION
# from ..tests.test_mixins import SubjectMixin
#
# from m... | botswana-harvard/bcpp-subject | bcpp_subject/tests/test_subject_helper.py | Python | gpl-3.0 | 51,167 | [
"VisIt"
] | e1d5651ba006a770a524f22900789d50625d98e7c30f21905172a493b51dc709 |
#!/usr/bin/python
# Extract Compounds' Features by RDKit.
# Songpeng Zu /zusongpeng@gmail.com/
#-- Import packages
# Import numpy and pandas for data structures in python
import numpy as np
from pandas import DataFrame, Series
import pandas as pd
# Import rdkit package for chemical feature extraction.
from rdkit imp... | biotcm/PICheM | ChemSpace/ComFeatureExtract_RDKit.py | Python | mit | 10,211 | [
"RDKit"
] | 5b0c36b4bf6e7615b96ac1550f7a9605169dcbfe6f66a6803fbccc3e3a5a8c9f |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | krafczyk/spack | var/spack/repos/builtin/packages/r-kegg-db/package.py | Python | lgpl-2.1 | 1,645 | [
"Bioconductor"
] | 40fb0aa139483a0100246cf625c4ca19d7929bdd79ea4535dbe1af1e54bcdd59 |
import discord
from discord.ext import commands
from .utils.chat_formatting import *
from random import randint
from random import choice as randchoice
import datetime
import time
import aiohttp
import asyncio
settings = {"POLL_DURATION" : 60}
class General:
"""General commands."""
def __init__(self, bot):
... | pkkao/musicbot | cogs/general.py | Python | gpl-3.0 | 19,622 | [
"MOOSE"
] | b34db1684f740ba7f6ab538371df6a8735e6dd67fa885dd5bb4f8ae4a27a1fe5 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkHierarchicalDataGroupFilter(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkHierarchicalDataGroupFilter.py | Python | bsd-3-clause | 526 | [
"VTK"
] | 6ac33d439775731f734dd9f422469cf4e6c6839e05b518aee893ac180e2ebba8 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
class Migration(migrations.Migration):
dependencies = [
('visit', '0053_auto_20150811_1259'),
]
operations = [
migrations.AddField(
model_name='issueprek',
na... | koebbe/homeworks | visit/migrations/0054_auto_20150811_1304.py | Python | mit | 568 | [
"VisIt"
] | a10958b3637f164dd16170fbcccd41045ea8ddf5063effe1658ba14b15db8b55 |
import re
import string
import pysam
import matplotlib
import pandas as pd
from collections import defaultdict
from collections import OrderedDict
import argparse
import itertools
matplotlib.use('pdf')
import matplotlib.pyplot as plt # noqa: E402
class MismatchFrequencies:
'''Iterate over a SAM/BAM alignment fi... | chamaelj/tools-artbio | tools/mismatch_frequencies/mismatch_frequencies.py | Python | mit | 14,573 | [
"pysam"
] | c0349f98fd640c3ee5c9b5befba6d7f2dbfcc4e91f96a8e4fb989a5209293daf |
# this DeVIDE snippet will determine the surface area of all selected
# 3D objects in a marked slice3dVWR
# in short:
# 1. right click on a slice3dVWR in the graphEditor
# 2. select "Mark Module" from the drop-down menu
# 3. accept "slice3dVWR" as suggestion for the mark index name
# 4. execute this snippet
import vt... | nagyistoce/devide | snippets/pdSurfaceArea.py | Python | bsd-3-clause | 995 | [
"VTK"
] | 4565e4b8d5b58058a4244ed5172367816ad42a0e2cbbad67e18d8e839ca14c41 |
#!/usr/bin/env python
# This example demonstrates the use of vtkLabeledDataMapper. This
# class is used for displaying numerical data from an underlying data
# set. In the case of this example, the underlying data are the point
# and cell ids.
import vtk
# Create a selection window. We will display the point and ... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Examples/Annotation/Python/labeledMesh.py | Python | gpl-3.0 | 4,428 | [
"VTK"
] | dec22a10759c7d8a822af792bdc79b5500abf074c7ba6d2c054dd7bc56458423 |
""" Module to looks for a specified pattern in a given AST. """
from ast import AST, iter_fields, NodeVisitor, Dict, Set
from itertools import permutations
from math import isnan
MAX_UNORDERED_LENGTH = 10
class DamnTooLongPattern(Exception):
""" Exception for long dict/set comparison to reduce compile time. ""... | artas360/pythran | pythran/analyses/ast_matcher.py | Python | bsd-3-clause | 6,976 | [
"VisIt"
] | c2b27c412b18bb159c70f6148f2505aa25ffd74732f2d1a0ed2d185fdbee326a |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | tlsantos/icecreamratings_project | config/urls.py | Python | bsd-3-clause | 1,293 | [
"VisIt"
] | fe5e4fe9cf20288b9146438115ccc3a74a9ee36a688afdd3bb05f48a398a2915 |
#!/usr/bin/env python3
#
# Script to assert proper occupations in VASP calculation using ASE
# by Patrick Melix
# 2021/06/15
#
from ase.calculators.vasp.vasp import Vasp
import os
import numpy as np
def main(path):
assert os.path.isdir(path), "Given path is not a directory"
calc = Vasp(directory=path)
xml ... | patrickmelix/Python4ChemistryTools | vasp-check.py | Python | mit | 1,484 | [
"ASE",
"VASP"
] | deb986f7e3ea568eb25c8b3ff6530c1d57e48781fbac590dcd4e59d41bfae7d9 |
import ocl
import camvtk
import time
import vtk
import datetime
import math
def drawBB(myscreen, bb):
lines=[]
# x-direction lines, red color
lines.append( camvtk.Line( p1=(bb.minpt.x, bb.minpt.y, bb.minpt.z), p2=(bb.maxpt.x, bb.minpt.y, bb.minpt.z), color=camvtk.red) )
lines.append( camvtk.Line( p1=(b... | tectronics/opencamlib | scripts/ocl_bounding-box.py | Python | gpl-3.0 | 3,245 | [
"VTK"
] | d184530a0ebb1bf481db7e5cc3dfbdb3140f555929d46a0330b31ed6ef856cab |
# encoding: utf-8
from __future__ import unicode_literals
import difflib
from textwrap import dedent
from kinko.types import StringType, ListType, VarNamedArgs, Func, Record, Option
from kinko.types import IntType, Union, Markup, NamedArg, BoolType
from kinko.compat import _exec_in, PY3, text_type_name
from kinko.loo... | vmagamedov/kinko | tests/test_python.py | Python | bsd-3-clause | 14,825 | [
"VisIt"
] | 4072044be4121ef85469c2652b4c83b5b8e30089815fdfe17676fa6a9f30d9ce |
#!/usr/bin/env python
import glob
from pyraf import iraf
import os
def runimedit(mfile,outfile1,nframe):
continueWithProgram=1
continueWithObject=1
repeatflag=1
while (repeatflag > 0.1):
iraf.display(mfile,frame=nframe, fill='yes')
print mfile
print 'Running imedit to mask o... | rfinn/LCS | paper1code/LCSellipse24.py | Python | gpl-3.0 | 9,365 | [
"Galaxy"
] | 45a72baea444bdc3be4a3de06e6633c82ee91f20ae08d9593f68411dfc3e1015 |
# ===============================================================================
# Copyright 2011 Jake Ross
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licens... | UManPychron/pychron | pychron/lasers/laser_managers/fusions_laser_manager.py | Python | apache-2.0 | 31,776 | [
"Gaussian"
] | 48d2e65040f2cdfc7bb612f6d71d85f87db5fad7b40641e02e6ab81a01816166 |
#
# Copyright (C) 2008, Brian Tanner
#
#http://rl-glue-ext.googlecode.com/
#
# Licensed under the Apache License, Version 2.0 (the "License")
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | okkhoy/mo-rlglue-python-codec | tests/test_empty_experiment.py | Python | mit | 2,574 | [
"Brian"
] | bbe714d92dc338230605d50b275157126af94cede87b6a58b10508b4e9323c5e |
##
# Copyright 2009-2020 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | pescobar/easybuild-easyblocks | easybuild/easyblocks/f/ferret.py | Python | gpl-2.0 | 8,490 | [
"NetCDF"
] | bbb3e17043271e2f69b05f7ca29cae35de016dfe15c91a00847107b2615e82a0 |
# Copyright (c) 2016-2017 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2016 Moises Lopez <moylop260@vauxoo.com>
# Copyright (c) 2017 hippo91 <guillaume.peillex@gmail.com>
# Licensed under the GPL: https://www.gnu.org/licenses/old-licenses/gpl-2.0.html
# For details: https://github.com/PyCQA/pylint/blob/master/... | AtomLinter/linter-pylama | bin/deps/pylint/extensions/mccabe.py | Python | mit | 5,962 | [
"VisIt"
] | ecc23656c1d80975caecf07118e3413ba11fd5ae6db99de7632fbe0908f572da |
import os
import sys
from collections import defaultdict, OrderedDict
from copy import deepcopy
from operator import itemgetter, attrgetter
import numpy as np
import six
from pythomics.proteomics.config import CARBON_NEUTRON
from scipy import optimize
from scipy.signal import convolve, kaiser
if os.environ.get('PYQUA... | pandeylab/pyquant | pyquant/peaks.py | Python | mit | 33,361 | [
"Gaussian"
] | 7bc0618d02fd06acad66cef5709c82acce7dfa8be3a32a2873bee0a2d0ea3679 |
from utils import *
from particleDataStructure import *
from prob_motion import *
from normalise_resample import *
import random, math
speed = 150
mymap = Map()
initMap(mymap)
K = 0.000014
s3 = PORT_3
enableSensor(s3, TYPE_SENSOR_ULTRASONIC_CONT)
# Returns how likely the x,y corresponds with sonar reading
def calcul... | andrei-alpha/robotics | old/moveMCL.py | Python | mit | 2,710 | [
"Gaussian"
] | 5218c17e53b4f5e69ec9aff183ac38d13f0c11c53dc3f2ffdd2b1c1ce9251fe4 |
#!/usr/bin/python
import string
class BinNode:
def __init__(self, value, left=None, right=None):
#types of node
self.OR = 1
self.AND = 2
self.EXP = 3 # '^' or exponent
self.EQ = 4 # ==
self.ATTR = 0
#OF = '' # anything above 1 and 2
if(isinstance(value, str)):
self.type = self.ATTR
self.a... | lferr/charm | charm/toolbox/zknode.py | Python | lgpl-3.0 | 1,616 | [
"VisIt"
] | 53de769697d1e76e4bf00cca86f5e44c79c86a739e361cfd6971953c9fb18b32 |
# Copyright 2019 Brian Quinlan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writin... | brianquinlan/learn-machine-learning | well_bouncer/learn.py | Python | mit | 7,448 | [
"Brian"
] | d5eb95ac4487d180dba529e952721b97f9f76b3e85a2356328a911dbdcd177af |
try:
from setuptools import setup
except ImportError:
from distutils.core import setup
from distutils.extension import Extension
setup(
name='PEAKachu',
version='0.2.0',
packages=['peakachulib'],
author='Thorsten Bischler',
author_email='thorsten.bischler@uni-wuerzburg.de',
description=... | tbischler/PEAKachu | setup.py | Python | isc | 1,092 | [
"Biopython",
"pysam"
] | aedb8219f923383e63de8b1728ad66665fa8e43ff351d4a89bcab4cf05948c7a |
import os
import unittest
from cclib.parser import ccData
from cclib.bridge import cclib2openbabel
class OpenbabelTest(unittest.TestCase):
"""Tests for the cclib2openbabel bridge in cclib."""
def setUp(self):
self.path = os.path.abspath(os.path.dirname(__file__))
def test_xyz_uracyl(self):
... | ghutchis/cclib | test/bridge/testopenbabel.py | Python | lgpl-2.1 | 540 | [
"cclib"
] | 24996af8e92841fc5088d4ee5f76a9df8994ccee4148f76322a46dfa73bf98bc |
""" CStoJSONSynchronizer
Module that keeps the pilot parameters file synchronized with the information
in the Operations/Pilot section of the CS. If there are additions in the CS,
these are incorporated to the file.
The module uploads to a web server the latest version of the pilot scripts.
"""
import json
i... | Andrew-McNab-UK/DIRAC | WorkloadManagementSystem/Utilities/PilotCStoJSONSynchronizer.py | Python | gpl-3.0 | 12,442 | [
"DIRAC"
] | 05223a771f9f8246310f3a78d0fd383f387564ec950f1c650f1a7a4a8c1bb19c |
#!/usr/bin/env python
import pysam
import sys
import argparse
import Tools
import pdb
from Bio import SeqIO
from Bio import SeqRecord
from Bio import Seq
ap = argparse.ArgumentParser(description="Select the read extending most into a gap.")
ap.add_argument("--sam", help="Input sam file, or stdin.", default="/dev/stdi... | yunlongliukm/chm1_scripts | SamToFasta.py | Python | mit | 647 | [
"pysam"
] | 06195cc0f3f0832a2e63e1a5f86b58270d398548697118108687d165dcd29bc3 |
from matplotlib import rcParams, rc
from spuriousRadioProbRange import probsOfGRP
from util import mpfit
from util.fitFunctions import gaussian
import matplotlib.pyplot as plt
import numpy as np
import matplotlib
import scipy.stats
import tables
import scipy.special
def fitGauss(xdata,ydata,yerr,flatLine=False):
... | bmazin/ARCONS-pipeline | examples/Pal2012-crab/enhancementPhase.py | Python | gpl-2.0 | 21,027 | [
"Gaussian"
] | b9bbf95e5dafa4e7d79e9c123d311d644b96ca71ea3c712110a32e9f25c92862 |
"""Grid climate for netcdf usage"""
import sys
import datetime
import numpy as np
from pandas import read_sql
from scipy.interpolate import NearestNDInterpolator
from pyiem import iemre
from pyiem.util import get_dbconnstr, ncopen, convert_value, logger
LOG = logger()
def generic_gridder(nc, df, idx):
"""
G... | akrherz/iem | scripts/iemre/grid_climate.py | Python | mit | 2,946 | [
"NetCDF"
] | b6da137b5cbb7c4f769035aec2f7d0bd81ed6cf061bfdcbb9d3ce1340cdc9a1f |
# $Id$
#
# Copyright (C) 2002-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" contains SMARTS d... | adalke/rdkit | rdkit/Chem/EState/AtomTypes.py | Python | bsd-3-clause | 4,035 | [
"RDKit"
] | 6858890cf480e7fb5566cb1a35456ba4e4ded73ba07515d4332c90601644414e |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
#
ANSIB... | andmos/ansible | lib/ansible/modules/network/avi/avi_hardwaresecuritymodulegroup.py | Python | gpl-3.0 | 3,651 | [
"VisIt"
] | 19e14f0cd9276be1bc11ac916bbe52d26e22aebbd1fa20368cbaedf1f78f6caf |
#Copyright (C) 2013 Alex Nitz
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.
#
# This program is distributed in the h... | tdent/pycbc | pycbc/strain/strain.py | Python | gpl-3.0 | 82,277 | [
"Gaussian"
] | a0595482cd8298fc82fdcb67aac100e302bf703c1ee36308bbde36f489c24d45 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/MooseDocs/test/extensions/test_sqa.py | Python | lgpl-2.1 | 35,712 | [
"MOOSE"
] | c054ee6608d29fc5082a89c0ddda0551192d07747bf7afe16076e112a9d749c1 |
#!/usr/bin/env python
# ----------------------------------------------------------------------
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
# https://www.lammps.org/ Sandia National Laboratories
# Steve Plimpton, sjplimp@sandia.gov
# -------------------------------------------------------------... | akohlmey/lammps | examples/COUPLE/lammps_nwchem/nwchem_wrap.py | Python | gpl-2.0 | 12,646 | [
"CRYSTAL",
"LAMMPS",
"NWChem"
] | 4c7489d08bd9aa84c772c37726b38c35c0af240681e58ff7352406fdf15a6574 |
import director.applogic as app
from director import lcmUtils
from director import transformUtils
from director import visualization as vis
from director import filterUtils
from director import drcargs
from director.shallowCopy import shallowCopy
from director.timercallback import TimerCallback
from director import vtk... | RobotLocomotion/director | src/python/director/cameraview.py | Python | bsd-3-clause | 30,568 | [
"VTK"
] | 0366551440e77fe7af4b7009cb2fbaa1028e3483a35d11d03c5c14e9e2680e44 |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/view/export/outlook.py | Python | gpl-2.0 | 1,743 | [
"VisIt"
] | 44ebcad5c4671a7945c7adcf899a766d2d3e1a5e2d1855dc041bd96b6dfce295 |
"""The morph-tool command line launcher."""
import logging
import click
import matplotlib.pyplot as plt
from neurom import load_neuron
from neurom.view.plotly import draw as plotly_draw
from neurom.viewer import draw as pyplot_draw
logging.basicConfig()
logger = logging.getLogger('morph_tool')
logger.setLevel(loggin... | wizmer/NeuroM | neurom/apps/cli.py | Python | bsd-3-clause | 1,374 | [
"NEURON"
] | 8d6f423da9c4dff3a9f953421495adf6a8b0b9aac5b8812c00be0a80fad83afc |
# -*- coding: utf-8 -*-
"""
End-to-end tests related to the cohort management on the LMS Instructor Dashboard
"""
from datetime import datetime
from pytz import UTC, utc
from bok_choy.promise import EmptyPromise
from nose.plugins.attrib import attr
from common.test.acceptance.tests.discussion.helpers import CohortTes... | TheMOOCAgency/edx-platform | common/test/acceptance/tests/discussion/test_cohort_management.py | Python | agpl-3.0 | 54,332 | [
"VisIt"
] | cd82999053f41bb70fa30654e4c04c9c9b43a3decf9a3389c56efddf6151c29c |
from collections import OrderedDict
from ..ordered_collection import OrderedCollection
class VisitCollectionError(Exception):
pass
class VisitCollection(OrderedCollection):
key = 'code'
ordering_attr = 'timepoint'
def timepoint_dates(self, dt=None):
"""Returns an ordered dictionary of vis... | botswana-harvard/edc-visit-schedule | edc_visit_schedule/schedule/visit_collection.py | Python | gpl-2.0 | 920 | [
"VisIt"
] | ce629bf44a2f8ae4a0df32fde56cdca77266ee9cbb229b85adcbdd3c3f7adc82 |
########################################################################
# This example illustrates molecular transport of an oscillatory reaction
# system, along a closed-end cylinder. Here all the molecules are
#, transported, a left to right and b and s right to left.
###############################################... | BhallaLab/moose-examples | tutorials/Rdesigneur/ex7.5_bidirectional_transport.py | Python | gpl-2.0 | 1,294 | [
"MOOSE"
] | 30f2a8cfa7cf7abd401c394133eec56b62648719024f046fc678f28116983fc7 |
import yaml
import argparse
import time
from sirius import save_state, Logger
from sirius.ot import ApplyHamiltonian, Energy
logger = Logger()
def validate_config(dd):
"""
Using voluptuous to make sure that the config is valid and
populate missing entries by their default values.
"""
from voluptu... | electronic-structure/sirius | python_module/sirius/nlcg/__init__.py | Python | bsd-2-clause | 6,272 | [
"DIRAC",
"Gaussian"
] | 7521705bb302ffcd31d2f4e477d4317127e3b9ef60ab527fa2b43eefe58f1b34 |
from operator import itemgetter
import networkx as nx
from tater import Node, NodeList, Visitor
class DiGraphRenderer(Visitor):
def __init__(self):
self.G = nx.DiGraph()
def maybe_add_nodes(self, *nodes):
G = self.G
for node in nodes:
if node['ident'] not in G.node:
... | asamended/python-asamended | asamended/uscode/node.py | Python | bsd-3-clause | 3,106 | [
"VisIt"
] | d37a9eaf0cab785fe0381461468d73968eb8d0f9cfab17e665092f905023e0de |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under th... | alejob/mdanalysis | package/MDAnalysis/analysis/encore/clustering/cluster.py | Python | gpl-2.0 | 9,567 | [
"MDAnalysis"
] | e34a656eeb7d0fb7ca0ef2b6e3f1c4b076ecbb90b5a2e20184e212a06f802444 |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2014 Brian Douglass bhdouglass@gmail.com
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Softwa... | bhdouglass/agui | agui/backends/gtk/widgets/button.py | Python | gpl-3.0 | 1,417 | [
"Brian"
] | 8ccbded77b38658fcb291a65b9c6ff3db5d9b2408ef7138c3b3880edd65470a0 |
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
"""Utility functions and classes."""
import os
import re
import sys
from operator import mul
from math import sqrt, exp
import numpy as np
from numpy import linalg
import _gpaw
from gpaw import debug
elementwise_multiply... | ajylee/gpaw-rtxs | gpaw/utilities/__init__.py | Python | gpl-3.0 | 10,019 | [
"GPAW"
] | a170570f9eb6bb2a690b50854a017438c613a460fa91474b0265d83b63b0c204 |
import os
from nose import tools as nt
import numpy as np
import subprocess
from neurom.apps.cut_plane_detection import find_cut_plane, _get_probabilities, _create_1d_distributions
from neurom.core import Neuron
from neurom import load_neuron
def test_empty_neuron():
result = find_cut_plane(Neuron())
nt.ass... | juanchopanza/NeuroM | neurom/tests/test_cut_plane_detection.py | Python | bsd-3-clause | 2,236 | [
"NEURON"
] | 6a25acc47d1847e12749f311c4f6714b405e45b7fa7b82e40d7121f77a0c3382 |
#!/usr/bin/env python
__author__ = 'Mike McCann'
__copyright__ = '2013'
__license__ = 'GPL v3'
__contact__ = 'mccann at mbari.org'
__doc__ = '''
Master loader for all October 2013 SIMZ activities.
Mike McCann
MBARI 24 October 2013
@var __date__: Date of last svn commit
@undocumented: __doc__ parser
@status... | josephmfaulkner/stoqs | stoqs/loaders/MolecularEcology/loadSIMZ_oct2013.py | Python | gpl-3.0 | 6,213 | [
"NetCDF"
] | 77ac65c9e7cfa66fded027e0f18e93254e4a9524cb2a387b2670cc3ed5aaebdb |
#!/usr/bin/env python
#
# Electrum - Lightweight Bitcoin Client
# Copyright (C) 2015 Thomas Voegtlin
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation files
# (the "Software"), to deal in the Software without restriction,
# including without... | spesmilo/electrum | electrum/plugins/trustedcoin/qt.py | Python | mit | 13,329 | [
"VisIt"
] | a6461c2e33b133829ef39ff19295264ba4d0c65b1fe282930e5b4b42ecc2c540 |
from pylab import *
import numpy as np
from numba import *
from numpy import random
def cc(T1, T2, width=.02, bin=.001, T=None):
n = int(np.ceil(width / bin)) # Histogram length
if (len(T1) == 0) or (len(T2) == 0): # empty spike train
return None
i = 0
j = 0
l = []
for t in T1:
... | rossant/spiky | experimental/cc2.py | Python | bsd-3-clause | 1,820 | [
"Brian"
] | e2d506495073b07becf7955ab360cead8ec642488e89ef0ea01afd5dcff16fe0 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
from __future__ import absolute_import, print_function
"""
This module provides classes used to enumerate surface sites
and to find adsorption sites on slabs
"... | aykol/pymatgen | pymatgen/analysis/adsorption.py | Python | mit | 22,646 | [
"Jmol",
"pymatgen"
] | aa00daade4c5e097441999073cadd2730d4fd8b0ca08df7695ae86073edcf52f |
#!/bin/env python
"""
Module openmm.unit.standard_dimensions
Definition of principal dimensions: mass, length, time, etc.
This is part of the OpenMM molecular simulation toolkit originating from
Simbios, the NIH National Center for Physics-Based Simulation of
Biological Structures at Stanford, funded under the NIH Ro... | mdtraj/mdtraj | mdtraj/utils/unit/standard_dimensions.py | Python | lgpl-2.1 | 2,372 | [
"OpenMM"
] | 4fbc77b632f20639692a209b4ca5780d83d523180bcde5d9c25febf4275beeff |
import numpy as np
from ase.optimize.optimize import Dynamics
from ase.optimize.fire import FIRE
from ase.units import kB
from ase.parallel import world
from ase.io.trajectory import PickleTrajectory
class BasinHopping(Dynamics):
"""Basin hopping algorythm.
After Wales and Doye, J. Phys. Chem. A, vol 101 (19... | slabanja/ase | ase/optimize/basin.py | Python | gpl-2.0 | 3,933 | [
"ASE"
] | a91112207085b1f486c4cfba41e31e0ce2513518e063cf46356e44648269ef12 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publi... | thica/ORCA-Remote | src/ORCA/definition/Definitions.py | Python | gpl-3.0 | 34,285 | [
"ORCA"
] | 207bc7204b1b873870d976f161c3ea94b99c1b3f99a75aaff737d7d6c864e53a |
"""This file can be loaded as a plugin for ParaView >= 5.6
Author: Bane Sullivan <banesulli@gmail.com>
"""
# This is module to import. It provides VTKPythonAlgorithmBase, the base class
# for all python-based vtkAlgorithm subclasses in VTK and decorators used to
# 'register' the algorithm with ParaView along with inf... | banesullivan/ParaViewGeophysics | snippets/PV_Composite_Writer.py | Python | bsd-3-clause | 11,351 | [
"ParaView",
"VTK"
] | 96cbfe0b09291509ea413c4f6275a7447b6e23f2c021d0f50e67cd592c08e952 |
# -----------------------------------------------------------------------------
# Download data:
# - Browser:
# http://midas3.kitware.com/midas/folder/10409 => VisibleMale/vm_head_mri.mha
# - Terminal
# curl "http://midas3.kitware.com/midas/download?folders=&items=235237" -o vm_head_mri.mha
# --------------... | Kitware/arctic-viewer | scripts/examples/vtk/medical/head-mri.py | Python | bsd-3-clause | 3,552 | [
"VTK"
] | 0e83ea4def918408987140bcab5f9e7c04cf39c9480685ca01b53bd0316a951d |
#Bayesian inference for simple linear regression with known noise variance
#The goal is to reproduce fig 3.7 from Bishop's book.
#We fit the linear model f(x,w) = w0 + w1*x and plot the posterior over w.
import superimport
import numpy as np
import matplotlib.pyplot as plt
import pyprobml_utils as pml
from scipy.s... | probml/pyprobml | scripts/bayes_linreg_2d_demo.py | Python | mit | 4,353 | [
"Gaussian"
] | fb2fdb670c816c0db9c95df52c70e409275150e72ec6ae8079140dfa34d28e74 |
import pysam
import argparse
import sys
import logging
import os
from asyncore import read
parser = argparse.ArgumentParser(description="Build soft clip position distribution in BAM file.",
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
DEBUG=False
NOT_DEBUG = not ... | shengqh/ngsperl | lib/QC/bamSoftClipPosition.py | Python | apache-2.0 | 3,130 | [
"pysam"
] | 3b34c8430ff8c89a2ba10f725bb930d12e49a571eca293c44da2ba186a1dc956 |
from __future__ import print_function
import numpy as np
from ase.units import Bohr
def attach_charges(atoms, fileobj='ACF.dat', displacement=1e-4):
"""Attach the charges from the fileobj to the Atoms."""
if isinstance(fileobj, str):
fileobj = open(fileobj)
sep = '---------------'
i = 0 # Coun... | suttond/MODOI | ase/io/bader.py | Python | lgpl-3.0 | 1,778 | [
"ASE"
] | e24cea503f13a050be15ce86bd7631966a502560a5e600fd99c0953120a71e16 |
# Copyright (c), Michael DeHaan <michael.dehaan@gmail.com>, 2012-2013
# Copyright (c), Toshio Kuratomi <tkuratomi@ansible.com> 2016
# Simplified BSD License (see licenses/simplified_bsd.txt or https://opensource.org/licenses/BSD-2-Clause)
SIZE_RANGES = {
'Y': 1 << 80,
'Z': 1 << 70,
'E': 1 << 60,
'P': 1... | Azulinho/ansible | lib/ansible/module_utils/basic.py | Python | gpl-3.0 | 111,995 | [
"VisIt"
] | 7cd9fddbf0872de793a429285cb0beb8506b453290a5a9056653d19efd2cd623 |
# Copyright (C) 2009 by Eric Talevich (eric.talevich@gmail.com)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""I/O function wrappers for phylogenetic tree formats.
This API follows the same seman... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/Phylo/_io.py | Python | gpl-2.0 | 2,579 | [
"Biopython"
] | 755a33d81b4ebdf7007017cea708812315bccb4ed42280aaf225f82cd082aed0 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | e-gob/plataforma-kioscos-autoatencion | scripts/ansible-play/.venv/lib/python2.7/site-packages/ansible/modules/network/avi/avi_cloudconnectoruser.py | Python | bsd-3-clause | 3,676 | [
"VisIt"
] | 01258c850ab8bc0d372518daf121e19c84d9457d96053576cb6d76e0f620eae3 |
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